The Nucleosome Family: Dynamic and Growing

Zlatanova, Jordanka; Bishop, Thomas C.; Victor, Jean–Marc; Jackson, Vaughn; Holde, Kensal van

doi:10.1016/j.str.2008.12.016

Cited by 161 publications

(159 citation statements)

References 97 publications

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“…Applying positive torsional stress shifts the equilibrium toward the positively crossed state. When the torsional stress reaches a critical value (see Supplementary Information), the nucleosomes undergo a structural transition, practically turning inside out through a chiral transition of the DNA superhelix (going from negatively to positively wrapped) while preserving the whole histone octamer; for further in-depth discussion, see Zlatanova et al (2009) [Fig. 2(a)].…”

Section: Nucleosome Dynamics In Response To Torsional Stressmentioning

confidence: 99%

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How are nucleosomes disrupted during transcription elongation?

Zlatanova

Victor

2009

HFSP Journal

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Section: Nucleosome Dynamics In Response To Torsional Stressmentioning

confidence: 99%

“…2. Some R-octasomes (or their derivative R-tetrasomes or R-hexasomes) may be lost altogether because H3/H4 tetramers prefer to bind negatively supercoiled DNA (Zlatanova et al, 2009). Thus, the positive torque in front of the advancing RNAP will produce a com- Figure 2.…”

Section: Proposed Physical Model For Nucleosome Disruptionmentioning

confidence: 99%

How are nucleosomes disrupted during transcription elongation?

Zlatanova

Victor

2009

HFSP Journal

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“…A large number of non-canonical structural states of the nucleosome were proposed and characterized experimentally to various degrees of detail (9,(12)(13)(14)(15)(16), but not at atomistic level.…”

Section: Introductionmentioning

confidence: 99%

“…An important class of non-canonical structures is partially assembled nucleosome states (PANS), some of which were proposed to occur on the nucleosome assembly/disassembly pathways (9,(15)(16)(17); compared to the intact nucleosome core particle (octasome), or its transient, partially unwrapped states (13,14), the PANS structures lack several histones. Importantly, the existence of PANS is a consequence of the modular nature of the nucleosome, facilitating the histone exchange process, which involves the removal of parts of the nucleosome or the entire nucleosome, followed by replacement with newly synthesized histones including variant histones.…”

Section: Introductionmentioning

confidence: 99%

Partially Assembled Nucleosome Structures at Atomic Detail

Rychkov

Ilatovskiy

Nazarov

et al. 2017

Biophysical Journal

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The evidence is now overwhelming that partially assembled nucleosome states (PANS) are as important as the canonical nucleosome structure for the understanding of how accessibility to genomic DNA is regulated in cells. We use a combination of molecular dynamics simulation and atomic force microscopy to deliver, in atomic detail, structural models of three key PANS: the hexasome (H2A$H2B)$(H3$H4) 2 , the tetrasome (H3$H4) 2 , and the disome (H3$H4). Despite fluctuations of the conformation of the free DNA in these structures, regions of protected DNA in close contact with the histone core remain stable, thus establishing the basis for the understanding of the role of PANS in DNA accessibility regulation. On average, the length of protected DNA in each structure is roughly 18 basepairs per histone protein. Atomistically detailed PANS are used to explain experimental observations; specifically, we discuss interpretation of atomic force microscopy, Fö rster resonance energy transfer, and small-angle x-ray scattering data obtained under conditions when PANS are expected to exist. Further, we suggest an alternative interpretation of a recent genome-wide study of DNA protection in active chromatin of fruit fly, leading to a conclusion that the three PANS are present in actively transcribing regions in a substantial amount. The presence of PANS may not only be a consequence, but also a prerequisite for fast transcription in vivo.

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“…Insight into the nature of partially unfolded NCP structures has been gleaned from in vitro studies of NCP assembly and disassembly. Intermediate species with partially unwrapped DNA (5, 7), disrupted histone-histone interfaces (8,9), and dissociation of one (hexasomes) or two (tetrasomes) H2A-H2B dimers have been reported (10)(11)(12). Some of these NCP intermediates have been directly connected to chromatin function in vivo.…”

mentioning

confidence: 99%

Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core

Chen

Tokuda

Topping

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

110

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The nucleosome core particle (NCP) is the basic structural unit for genome packaging in eukaryotic cells and consists of DNA wound around a core of eight histone proteins. DNA access is modulated through dynamic processes of NCP disassembly. Partly disassembled structures, such as the hexasome (containing six histones) and the tetrasome (four histones), are important for transcription regulation in vivo. However, the pathways for their formation have been difficult to characterize. We combine time-resolved (TR) small-angle X-ray scattering and TR-FRET to correlate changes in the DNA conformations with composition of the histone core during saltinduced disassembly of canonical NCPs. We find that H2A-H2B histone dimers are released sequentially, with the first dimer being released after the DNA has formed an asymmetrically unwrapped, teardrop-shape DNA structure. This finding suggests that the octasome-to-hexasome transition is guided by the asymmetric unwrapping of the DNA. The link between DNA structure and histone composition suggests a potential mechanism for the action of proteins that alter nucleosome configurations such as histone chaperones and chromatin remodeling complexes.G enome access is highly regulated through the hierarchical organization of proteins and nucleic acids within the cell nucleus. The nucleosome core particle (NCP) is the first level of this hierarchy (1) and contains two dimers of H2A-H2B histones and an (H3-H4) 2 tetramer that is assembled as a dimer of dimers. Around this symmetric octamer core, ∼146 base pairs of dsDNA are wrapped in ∼1.7 superhelical turns (1, 2). The NCP structure physically impedes access to DNA, but is dynamically modulated by numerous mechanisms: posttranslational modification (PTM) of histones, incorporation of histone variants, DNA sequence-dependent effects, and the actions of extrinsic protein factors (e.g., histone chaperones, ATP-dependent remodeling complexes, and histone PTM binding proteins) (3, 4).Studies of the intrinsic properties and dynamics of NCPs are critical for understanding how nuclear machinery gains DNA access in vivo (3,5,6). Insight into the nature of partially unfolded NCP structures has been gleaned from in vitro studies of NCP assembly and disassembly. Intermediate species with partially unwrapped DNA (5, 7), disrupted histone-histone interfaces (8, 9), and dissociation of one (hexasomes) or two (tetrasomes) H2A-H2B dimers have been reported (10-12). Some of these NCP intermediates have been directly connected to chromatin function in vivo. For example, the hexasome is formed by the action of RNA Pol II (13) and the essential histone chaperone FACT (14).In addition to equilibrium studies, the kinetics of nucleosome assembly and disassembly have been characterized by bulk and single-molecule methods, including Förster resonance energy transfer (FRET) (7,8,(15)(16)(17), atomic force microscopy (AFM) (9, 18), force spectroscopy (19-21), and small-angle X-ray scattering (SAXS) (10,22). Many studies focused primarily on specific DNA-histon...

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The Nucleosome Family: Dynamic and Growing

Cited by 161 publications

References 97 publications

How are nucleosomes disrupted during transcription elongation?

How are nucleosomes disrupted during transcription elongation?

Partially Assembled Nucleosome Structures at Atomic Detail

Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core

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